Starting phenix.real_space_refine on Fri Aug 22 18:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0t_41784/08_2025/8u0t_41784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0t_41784/08_2025/8u0t_41784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u0t_41784/08_2025/8u0t_41784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0t_41784/08_2025/8u0t_41784.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0t_41784/08_2025/8u0t_41784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0t_41784/08_2025/8u0t_41784.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4377 2.51 5 N 1134 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6761 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5342 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 34, 'TRANS': 640} Chain breaks: 1 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 14, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1292 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' ZN': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.91, per 1000 atoms: 0.28 Number of scatterers: 6761 At special positions: 0 Unit cell: (101, 96, 115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1211 8.00 N 1134 7.00 C 4377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.22 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.06 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.06 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.13 Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 90 " " NAG A 802 " - " ASN A 546 " " NAG A 803 " - " ASN A 53 " " NAG A 804 " - " ASN A 299 " " NAG A 805 " - " ASN A 329 " " NAG A 806 " - " ASN A 432 " " NAG A 807 " - " ASN A 82 " " NAG B 601 " - " ASN B 333 " " NAG B 602 " - " ASN B 360 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 391.7 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 808 " pdb="ZN ZN A 808 " - pdb=" NE2 HIS A 374 " 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 56.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.390A pdb=" N ASN A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.729A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.193A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.701A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.637A pdb=" N GLY A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.585A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.505A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.648A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 249 removed outlier: 4.385A pdb=" N GLU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.895A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.888A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 411 removed outlier: 3.882A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.603A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.656A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.873A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.665A pdb=" N LYS A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.715A pdb=" N PHE A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.981A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 659 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.939A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.023A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 491 through 494 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.580A pdb=" N GLU A 140 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.099A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.095A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 620 removed outlier: 7.046A pdb=" N SER A 680 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 344 through 348 Processing sheet with id=AA6, first strand: chain 'B' and resid 441 through 443 Processing sheet with id=AA7, first strand: chain 'B' and resid 462 through 463 326 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 5 1.19 - 1.36: 2136 1.36 - 1.52: 2887 1.52 - 1.68: 1866 1.68 - 1.85: 62 Bond restraints: 6956 Sorted by residual: bond pdb=" C GLU A 402 " pdb=" O GLU A 402 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.29e-02 6.01e+03 2.57e+02 bond pdb=" CA GLU A 402 " pdb=" CB GLU A 402 " ideal model delta sigma weight residual 1.529 1.326 0.203 1.63e-02 3.76e+03 1.55e+02 bond pdb=" C GLU A 406 " pdb=" O GLU A 406 " ideal model delta sigma weight residual 1.237 1.141 0.095 1.19e-02 7.06e+03 6.40e+01 bond pdb=" CD ARG A 134 " pdb=" NE ARG A 134 " ideal model delta sigma weight residual 1.458 1.566 -0.108 1.40e-02 5.10e+03 6.00e+01 bond pdb=" N ASN A 546 " pdb=" CA ASN A 546 " ideal model delta sigma weight residual 1.459 1.550 -0.091 1.32e-02 5.74e+03 4.77e+01 ... (remaining 6951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 9322 4.59 - 9.18: 141 9.18 - 13.77: 5 13.77 - 18.36: 0 18.36 - 22.95: 2 Bond angle restraints: 9470 Sorted by residual: angle pdb=" CD1 LEU B 475 " pdb=" CG LEU B 475 " pdb=" CD2 LEU B 475 " ideal model delta sigma weight residual 110.80 133.75 -22.95 2.20e+00 2.07e-01 1.09e+02 angle pdb=" CD1 LEU A 351 " pdb=" CG LEU A 351 " pdb=" CD2 LEU A 351 " ideal model delta sigma weight residual 110.80 133.46 -22.66 2.20e+00 2.07e-01 1.06e+02 angle pdb=" C ARG A 134 " pdb=" N PRO A 135 " pdb=" CA PRO A 135 " ideal model delta sigma weight residual 119.84 131.49 -11.65 1.25e+00 6.40e-01 8.69e+01 angle pdb=" N SER B 363 " pdb=" CA SER B 363 " pdb=" C SER B 363 " ideal model delta sigma weight residual 113.23 102.21 11.02 1.24e+00 6.50e-01 7.90e+01 angle pdb=" C ASN A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta sigma weight residual 119.19 127.76 -8.57 1.06e+00 8.90e-01 6.54e+01 ... (remaining 9465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3949 17.01 - 34.02: 190 34.02 - 51.04: 35 51.04 - 68.05: 11 68.05 - 85.06: 5 Dihedral angle restraints: 4190 sinusoidal: 1696 harmonic: 2494 Sorted by residual: dihedral pdb=" CB CYS B 469 " pdb=" SG CYS B 469 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual -86.00 -171.06 85.06 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 31.49 61.51 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" C GLU A 402 " pdb=" N GLU A 402 " pdb=" CA GLU A 402 " pdb=" CB GLU A 402 " ideal model delta harmonic sigma weight residual -122.60 -106.82 -15.78 0 2.50e+00 1.60e-01 3.98e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 942 0.137 - 0.274: 71 0.274 - 0.412: 17 0.412 - 0.549: 1 0.549 - 0.686: 2 Chirality restraints: 1033 Sorted by residual: chirality pdb=" CG LEU A 351 " pdb=" CB LEU A 351 " pdb=" CD1 LEU A 351 " pdb=" CD2 LEU A 351 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASN A 136 " pdb=" N ASN A 136 " pdb=" C ASN A 136 " pdb=" CB ASN A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 1030 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 82 " -0.083 2.00e-02 2.50e+03 8.13e-02 8.27e+01 pdb=" CG ASN A 82 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN A 82 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 82 " 0.117 2.00e-02 2.50e+03 pdb=" C1 NAG A 807 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 299 " 0.027 2.00e-02 2.50e+03 5.64e-02 3.19e+01 pdb=" C ASN A 299 " -0.098 2.00e-02 2.50e+03 pdb=" O ASN A 299 " 0.037 2.00e-02 2.50e+03 pdb=" N GLN A 300 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 402 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C GLU A 402 " 0.089 2.00e-02 2.50e+03 pdb=" O GLU A 402 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 403 " -0.029 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1952 2.81 - 3.33: 6011 3.33 - 3.86: 10777 3.86 - 4.38: 13352 4.38 - 4.90: 21852 Nonbonded interactions: 53944 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 808 " model vdw 2.291 2.230 nonbonded pdb=" O THR B 489 " pdb=" OG1 THR B 489 " model vdw 2.439 3.040 nonbonded pdb=" N SER B 363 " pdb=" N SER B 364 " model vdw 2.483 2.560 nonbonded pdb=" O ARG A 115 " pdb=" N SER A 118 " model vdw 2.492 3.120 nonbonded pdb=" N GLN A 139 " pdb=" N GLU A 140 " model vdw 2.525 2.560 ... (remaining 53939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.425 6972 Z= 0.815 Angle : 1.434 22.949 9509 Z= 0.954 Chirality : 0.089 0.686 1033 Planarity : 0.007 0.093 1200 Dihedral : 10.776 80.773 2568 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.74 % Favored : 97.14 % Rotamer: Outliers : 0.47 % Allowed : 3.11 % Favored : 96.42 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.27), residues: 839 helix: -0.93 (0.23), residues: 397 sheet: 0.79 (0.62), residues: 59 loop : -0.50 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.025 0.004 TYR A 516 PHE 0.015 0.003 PHE A 523 TRP 0.020 0.004 TRP A 163 HIS 0.017 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01337 ( 6956) covalent geometry : angle 1.40088 ( 9470) SS BOND : bond 0.09034 ( 6) SS BOND : angle 7.83215 ( 12) hydrogen bonds : bond 0.22993 ( 326) hydrogen bonds : angle 7.99954 ( 915) metal coordination : bond 0.42543 ( 1) link_NAG-ASN : bond 0.06930 ( 9) link_NAG-ASN : angle 3.00185 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.320 Fit side-chains REVERT: A 259 THR cc_start: 0.7826 (m) cc_final: 0.7264 (p) REVERT: B 396 ASP cc_start: 0.8112 (m-30) cc_final: 0.7872 (m-30) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.0892 time to fit residues: 17.3273 Evaluate side-chains 89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147408 restraints weight = 7729.217| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.28 r_work: 0.3478 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6972 Z= 0.158 Angle : 0.624 11.908 9509 Z= 0.327 Chirality : 0.054 0.879 1033 Planarity : 0.005 0.033 1200 Dihedral : 4.972 32.022 1115 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.56 % Allowed : 8.40 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.29), residues: 839 helix: 0.44 (0.26), residues: 405 sheet: 0.81 (0.63), residues: 58 loop : -0.24 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 652 TYR 0.023 0.002 TYR A 385 PHE 0.017 0.002 PHE A 327 TRP 0.013 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6956) covalent geometry : angle 0.59271 ( 9470) SS BOND : bond 0.00416 ( 6) SS BOND : angle 1.56398 ( 12) hydrogen bonds : bond 0.05627 ( 326) hydrogen bonds : angle 5.11262 ( 915) metal coordination : bond 0.00200 ( 1) link_NAG-ASN : bond 0.00720 ( 9) link_NAG-ASN : angle 3.55458 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 THR cc_start: 0.8352 (m) cc_final: 0.7900 (p) REVERT: A 292 ASP cc_start: 0.8346 (t0) cc_final: 0.8138 (t0) REVERT: A 355 ASP cc_start: 0.8500 (t0) cc_final: 0.8192 (t0) REVERT: A 408 MET cc_start: 0.8547 (mmt) cc_final: 0.8203 (mmt) REVERT: B 396 ASP cc_start: 0.8543 (m-30) cc_final: 0.8304 (m-30) REVERT: B 446 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.8076 (ttt-90) REVERT: B 489 THR cc_start: 0.8124 (p) cc_final: 0.7610 (p) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.0761 time to fit residues: 10.5049 Evaluate side-chains 94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.178637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143977 restraints weight = 7753.311| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.08 r_work: 0.3431 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6972 Z= 0.173 Angle : 0.639 15.704 9509 Z= 0.324 Chirality : 0.048 0.511 1033 Planarity : 0.005 0.044 1200 Dihedral : 4.813 30.123 1113 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.02 % Allowed : 9.18 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.29), residues: 839 helix: 0.74 (0.26), residues: 407 sheet: 0.66 (0.66), residues: 58 loop : -0.44 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 169 TYR 0.025 0.002 TYR A 385 PHE 0.016 0.002 PHE A 573 TRP 0.013 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6956) covalent geometry : angle 0.61169 ( 9470) SS BOND : bond 0.00702 ( 6) SS BOND : angle 2.34182 ( 12) hydrogen bonds : bond 0.05480 ( 326) hydrogen bonds : angle 4.84098 ( 915) metal coordination : bond 0.00160 ( 1) link_NAG-ASN : bond 0.00662 ( 9) link_NAG-ASN : angle 3.15754 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8776 (m) cc_final: 0.8275 (p) REVERT: A 288 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6657 (mmtt) REVERT: A 322 HIS cc_start: 0.8295 (m-70) cc_final: 0.8047 (m-70) REVERT: A 408 MET cc_start: 0.8679 (mmt) cc_final: 0.8328 (mmt) REVERT: B 396 ASP cc_start: 0.8724 (m-30) cc_final: 0.8464 (m-30) REVERT: B 446 ARG cc_start: 0.8408 (ttt-90) cc_final: 0.8080 (ttt-90) REVERT: B 489 THR cc_start: 0.8269 (p) cc_final: 0.7810 (p) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.0798 time to fit residues: 10.4315 Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 11 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143434 restraints weight = 7723.254| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.04 r_work: 0.3443 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6972 Z= 0.119 Angle : 0.553 14.136 9509 Z= 0.277 Chirality : 0.045 0.437 1033 Planarity : 0.004 0.035 1200 Dihedral : 4.245 37.097 1113 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.71 % Allowed : 10.11 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.29), residues: 839 helix: 1.07 (0.26), residues: 407 sheet: 0.76 (0.66), residues: 58 loop : -0.31 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.020 0.001 TYR A 654 PHE 0.011 0.001 PHE A 369 TRP 0.009 0.001 TRP A 203 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6956) covalent geometry : angle 0.51665 ( 9470) SS BOND : bond 0.00789 ( 6) SS BOND : angle 2.24872 ( 12) hydrogen bonds : bond 0.04254 ( 326) hydrogen bonds : angle 4.50238 ( 915) metal coordination : bond 0.00101 ( 1) link_NAG-ASN : bond 0.00492 ( 9) link_NAG-ASN : angle 3.43533 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7109 (tt0) REVERT: A 259 THR cc_start: 0.8568 (m) cc_final: 0.8057 (p) REVERT: A 269 ASP cc_start: 0.8081 (t0) cc_final: 0.7854 (t0) REVERT: A 288 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6617 (mmtt) REVERT: A 322 HIS cc_start: 0.8130 (m-70) cc_final: 0.7855 (m-70) REVERT: B 396 ASP cc_start: 0.8592 (m-30) cc_final: 0.8319 (m-30) REVERT: B 446 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.7988 (ttt-90) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.0842 time to fit residues: 11.5963 Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.0040 chunk 80 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118330 restraints weight = 7824.791| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.27 r_work: 0.3123 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6972 Z= 0.129 Angle : 0.546 13.873 9509 Z= 0.276 Chirality : 0.044 0.388 1033 Planarity : 0.004 0.037 1200 Dihedral : 4.135 38.322 1113 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.71 % Allowed : 10.58 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.30), residues: 839 helix: 1.19 (0.26), residues: 407 sheet: 0.88 (0.66), residues: 58 loop : -0.33 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.022 0.002 TYR A 654 PHE 0.025 0.001 PHE A 327 TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6956) covalent geometry : angle 0.52221 ( 9470) SS BOND : bond 0.00766 ( 6) SS BOND : angle 2.09253 ( 12) hydrogen bonds : bond 0.04538 ( 326) hydrogen bonds : angle 4.46888 ( 915) metal coordination : bond 0.00209 ( 1) link_NAG-ASN : bond 0.00394 ( 9) link_NAG-ASN : angle 2.75219 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6834 (tt0) REVERT: A 259 THR cc_start: 0.8750 (m) cc_final: 0.8168 (p) REVERT: A 322 HIS cc_start: 0.8300 (m-70) cc_final: 0.8080 (m-70) REVERT: A 376 MET cc_start: 0.8335 (mmm) cc_final: 0.7973 (mmm) REVERT: A 408 MET cc_start: 0.8435 (mmt) cc_final: 0.8154 (mmm) REVERT: A 480 MET cc_start: 0.8811 (ptm) cc_final: 0.8610 (mtp) REVERT: B 396 ASP cc_start: 0.8614 (m-30) cc_final: 0.8276 (m-30) REVERT: B 446 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7805 (ttt-90) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.0836 time to fit residues: 10.0887 Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 0.0670 chunk 67 optimal weight: 0.0470 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.0570 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 54 optimal weight: 0.8980 overall best weight: 0.1612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123982 restraints weight = 7843.123| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.23 r_work: 0.3193 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 6972 Z= 0.096 Angle : 0.487 13.203 9509 Z= 0.246 Chirality : 0.042 0.301 1033 Planarity : 0.004 0.034 1200 Dihedral : 3.744 35.899 1113 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.71 % Allowed : 10.73 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.30), residues: 839 helix: 1.48 (0.26), residues: 408 sheet: 0.84 (0.65), residues: 58 loop : -0.10 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.020 0.001 TYR A 654 PHE 0.017 0.001 PHE A 327 TRP 0.009 0.001 TRP A 203 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6956) covalent geometry : angle 0.46887 ( 9470) SS BOND : bond 0.00746 ( 6) SS BOND : angle 1.84451 ( 12) hydrogen bonds : bond 0.03519 ( 326) hydrogen bonds : angle 4.29372 ( 915) metal coordination : bond 0.00075 ( 1) link_NAG-ASN : bond 0.00322 ( 9) link_NAG-ASN : angle 2.22629 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6808 (tt0) REVERT: A 69 TRP cc_start: 0.7988 (t-100) cc_final: 0.7771 (t-100) REVERT: A 259 THR cc_start: 0.8682 (m) cc_final: 0.8080 (p) REVERT: A 288 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6536 (mmtp) REVERT: A 322 HIS cc_start: 0.8124 (m-70) cc_final: 0.7907 (m-70) REVERT: A 376 MET cc_start: 0.8328 (mmm) cc_final: 0.8095 (mmm) REVERT: A 408 MET cc_start: 0.8334 (mmt) cc_final: 0.8041 (mmm) REVERT: B 396 ASP cc_start: 0.8614 (m-30) cc_final: 0.8287 (m-30) REVERT: B 446 ARG cc_start: 0.8352 (ttt-90) cc_final: 0.8092 (ttt-90) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.0782 time to fit residues: 10.1619 Evaluate side-chains 89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 67 optimal weight: 0.0170 chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121031 restraints weight = 7704.398| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.16 r_work: 0.3138 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 6972 Z= 0.105 Angle : 0.496 13.575 9509 Z= 0.251 Chirality : 0.042 0.294 1033 Planarity : 0.004 0.036 1200 Dihedral : 3.618 33.200 1113 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.09 % Allowed : 11.20 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.30), residues: 839 helix: 1.54 (0.26), residues: 409 sheet: 0.80 (0.65), residues: 58 loop : -0.13 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.023 0.001 TYR A 654 PHE 0.010 0.001 PHE A 369 TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6956) covalent geometry : angle 0.48079 ( 9470) SS BOND : bond 0.00721 ( 6) SS BOND : angle 1.85445 ( 12) hydrogen bonds : bond 0.03809 ( 326) hydrogen bonds : angle 4.24517 ( 915) metal coordination : bond 0.00095 ( 1) link_NAG-ASN : bond 0.00314 ( 9) link_NAG-ASN : angle 2.05146 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6831 (tt0) REVERT: A 259 THR cc_start: 0.8631 (m) cc_final: 0.8023 (p) REVERT: A 322 HIS cc_start: 0.8090 (m-70) cc_final: 0.7888 (m-70) REVERT: A 376 MET cc_start: 0.8141 (mmm) cc_final: 0.7899 (mmm) REVERT: A 557 MET cc_start: 0.9097 (tmm) cc_final: 0.8681 (ttp) REVERT: B 396 ASP cc_start: 0.8494 (m-30) cc_final: 0.8170 (m-30) REVERT: B 446 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.8070 (ttt-90) outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 0.0752 time to fit residues: 9.0483 Evaluate side-chains 88 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117802 restraints weight = 7856.412| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.12 r_work: 0.3093 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6972 Z= 0.138 Angle : 0.542 13.804 9509 Z= 0.275 Chirality : 0.044 0.307 1033 Planarity : 0.004 0.039 1200 Dihedral : 3.652 21.336 1113 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.40 % Allowed : 11.51 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.30), residues: 839 helix: 1.40 (0.26), residues: 408 sheet: 0.83 (0.65), residues: 58 loop : -0.23 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.024 0.002 TYR A 654 PHE 0.015 0.001 PHE A 369 TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6956) covalent geometry : angle 0.52745 ( 9470) SS BOND : bond 0.00806 ( 6) SS BOND : angle 2.04272 ( 12) hydrogen bonds : bond 0.04538 ( 326) hydrogen bonds : angle 4.37510 ( 915) metal coordination : bond 0.00171 ( 1) link_NAG-ASN : bond 0.00507 ( 9) link_NAG-ASN : angle 1.97476 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6903 (tt0) REVERT: A 259 THR cc_start: 0.8684 (m) cc_final: 0.8084 (p) REVERT: A 322 HIS cc_start: 0.8234 (m-70) cc_final: 0.8014 (m-70) REVERT: A 376 MET cc_start: 0.8098 (mmm) cc_final: 0.7859 (mmm) REVERT: B 396 ASP cc_start: 0.8479 (m-30) cc_final: 0.8171 (m-30) REVERT: B 446 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.8057 (ttt-90) outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 0.0842 time to fit residues: 9.7501 Evaluate side-chains 84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116230 restraints weight = 7870.256| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.49 r_work: 0.3078 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6972 Z= 0.145 Angle : 0.544 13.734 9509 Z= 0.277 Chirality : 0.044 0.318 1033 Planarity : 0.004 0.041 1200 Dihedral : 3.697 22.196 1113 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.24 % Allowed : 11.51 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.30), residues: 839 helix: 1.36 (0.26), residues: 408 sheet: 0.87 (0.64), residues: 58 loop : -0.26 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.024 0.002 TYR A 654 PHE 0.017 0.001 PHE A 369 TRP 0.011 0.001 TRP A 69 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6956) covalent geometry : angle 0.52914 ( 9470) SS BOND : bond 0.00797 ( 6) SS BOND : angle 2.04051 ( 12) hydrogen bonds : bond 0.04621 ( 326) hydrogen bonds : angle 4.39915 ( 915) metal coordination : bond 0.00176 ( 1) link_NAG-ASN : bond 0.00416 ( 9) link_NAG-ASN : angle 1.99869 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8690 (m) cc_final: 0.7983 (p) REVERT: A 269 ASP cc_start: 0.8184 (t0) cc_final: 0.7913 (t0) REVERT: A 322 HIS cc_start: 0.8316 (m-70) cc_final: 0.8107 (m-70) REVERT: B 396 ASP cc_start: 0.8488 (m-30) cc_final: 0.8145 (m-30) REVERT: B 446 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.8062 (ttt-90) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.0850 time to fit residues: 9.1293 Evaluate side-chains 83 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.177204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143754 restraints weight = 7636.958| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.91 r_work: 0.3471 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6972 Z= 0.121 Angle : 0.522 13.610 9509 Z= 0.266 Chirality : 0.043 0.300 1033 Planarity : 0.004 0.039 1200 Dihedral : 3.529 20.994 1113 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.09 % Allowed : 11.66 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.30), residues: 839 helix: 1.30 (0.26), residues: 415 sheet: 0.81 (0.65), residues: 57 loop : -0.24 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.025 0.001 TYR A 654 PHE 0.012 0.001 PHE A 369 TRP 0.013 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6956) covalent geometry : angle 0.50849 ( 9470) SS BOND : bond 0.00798 ( 6) SS BOND : angle 1.95814 ( 12) hydrogen bonds : bond 0.04211 ( 326) hydrogen bonds : angle 4.34849 ( 915) metal coordination : bond 0.00097 ( 1) link_NAG-ASN : bond 0.00380 ( 9) link_NAG-ASN : angle 1.90675 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7172 (tt0) REVERT: A 259 THR cc_start: 0.8709 (m) cc_final: 0.8188 (p) REVERT: A 322 HIS cc_start: 0.8208 (m-70) cc_final: 0.8000 (m-70) REVERT: A 323 MET cc_start: 0.7957 (mmt) cc_final: 0.7665 (mmm) REVERT: B 396 ASP cc_start: 0.8663 (m-30) cc_final: 0.8412 (m-30) REVERT: B 446 ARG cc_start: 0.8433 (ttt-90) cc_final: 0.8228 (ttt-90) outliers start: 7 outliers final: 7 residues processed: 82 average time/residue: 0.0847 time to fit residues: 9.6729 Evaluate side-chains 82 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 56 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0020 chunk 74 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.182324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148565 restraints weight = 7719.176| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.91 r_work: 0.3500 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 6972 Z= 0.105 Angle : 0.501 13.434 9509 Z= 0.256 Chirality : 0.042 0.275 1033 Planarity : 0.004 0.037 1200 Dihedral : 3.364 19.556 1113 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.09 % Allowed : 12.29 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.30), residues: 839 helix: 1.45 (0.26), residues: 417 sheet: 0.80 (0.66), residues: 57 loop : -0.16 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.026 0.001 TYR A 654 PHE 0.013 0.001 PHE A 369 TRP 0.014 0.001 TRP A 69 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6956) covalent geometry : angle 0.48888 ( 9470) SS BOND : bond 0.00789 ( 6) SS BOND : angle 1.83999 ( 12) hydrogen bonds : bond 0.03810 ( 326) hydrogen bonds : angle 4.28232 ( 915) metal coordination : bond 0.00091 ( 1) link_NAG-ASN : bond 0.00361 ( 9) link_NAG-ASN : angle 1.78031 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.23 seconds wall clock time: 35 minutes 13.46 seconds (2113.46 seconds total)